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Hosseinpour M, Ardalani F, Mohseni M, Beheshtian M, Arzhangi S, Ossareh S, Najmabadi H, Nobakht A, Kahrizi K, Broumand B. Targeted Next Generation Sequencing Revealed Novel Variants in the PKD1 and PKD2 Genes of Iranian Patients with Autosomal Dominant Polycystic Kidney Disease. ARCHIVES OF IRANIAN MEDICINE 2022; 25:600-608. [PMID: 37543885 PMCID: PMC10685772 DOI: 10.34172/aim.2022.95] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/10/2022] [Indexed: 08/07/2023]
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD), one of the common inherited disorders in humans, is characterized by the development and enlargement of renal cysts, often leading to end-stage renal disease (ESRD). In this study, Iranian ADPKD families were subjected to high-throughput DNA sequencing to find potential causative variants facilitating the way toward risk assessment and targeted therapy. METHODS Our protocol was based on the targeted next generation sequencing (NGS) panel previously developed in our center comprising 12 genes involved in PKD. This panel has been applied to investigate the genetic causes of 32 patients with a clinical suspicion of ADPKD. RESULTS We identified a total of 31 variants for 32 individuals, two of which were each detected in two individuals. Twenty-seven out of 31 detected variants were interpreted as pathogenic/likely pathogenic and the remaining 4 of uncertain significance with a molecular diagnostic success rate of 87.5%. Among these variants, 25 PKD1/2 pathogenic/likely pathogenic variants were detected in 32 index patients (78.1%), and variants of uncertain significance in four individuals (12.5% in PKD1/2). The majority of variants was identified in PKD1 (74.2%). Autosomal recessive PKD was identified in one patient, indicating the similarities between recessive and dominant PKD. In concordance with earlier studies, this biallelic PKD1 variant, p.Arg3277Cys, leads to rapidly progressive and severe disease with very early-onset ADPKD. CONCLUSION Our findings suggest that targeted gene panel sequencing is expected to be the method of choice to improve diagnostic and prognostic accuracy in PKD patients with heterogeneity in genetic background.
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Affiliation(s)
- Maryam Hosseinpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fariba Ardalani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Shahrzad Ossareh
- Division of Nephrology, Department of Medicine, Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Ali Nobakht
- Department of Nephrology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Behrooz Broumand
- Pars Advanced and Minimally Invasive Medical Manners Research Center, Pars Hospital, Tehran, Iran
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Kim H, Park HC, Ryu H, Kim H, Lee HS, Heo J, Lee C, Kim NKD, Park WY, Hwang YH, Lee KB, Oh KH, Oh YK, Ahn C. Genetic Characteristics of Korean Patients with Autosomal Dominant Polycystic Kidney Disease by Targeted Exome Sequencing. Sci Rep 2019; 9:16952. [PMID: 31740684 PMCID: PMC6861305 DOI: 10.1038/s41598-019-52474-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 09/30/2019] [Indexed: 12/25/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is one of the main causes of end-stage renal disease (ESRD). Genetic information is of the utmost importance in understanding pathogenesis of ADPKD. Therefore, this study aimed to demonstrate the genetic characteristics of ADPKD and their effects on renal function in 749 Korean ADPKD subjects from 524 unrelated families. Genetic studies of PKD1/2 were performed using targeted exome sequencing combined with Sanger sequencing in exon 1 of the PKD1 gene and a multiple ligation probe assay. The mutation detection rate was 80.7% (423/524 families, 331 mutations) and 70.7% was novel. PKD1 protein-truncating (PKD1-PT) genotype was associated with younger age at diagnosis, larger kidney volume, lower renal function compared to PKD1 non-truncating and PKD2 genotypes. The PKD1 genotype showed earlier onset of ESRD compared to PKD2 genotype (64.9 vs. 72.9 years old, P < 0.001). In frailty model controlled for age, gender, and familial clustering effect, PKD2 genotype had 0.2 times lower risk for reaching ESRD than PKD1-PT genotype (p = 0.037). In conclusion, our results suggest that genotyping can contribute to selecting rapid progressors for new emerging therapeutic interventions among Koreans.
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Affiliation(s)
- Hyunsuk Kim
- Department of Internal Medicine, Chuncheon Sacred Heart Hospital, Chuncheon, Korea
| | - Hayne Cho Park
- Department of Internal Medicine, Kangnam Sacred Heart Hospital, Seoul, Korea
| | - Hyunjin Ryu
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Hyunho Kim
- Center for Medical Innovation, Seoul National University Hospital, Seoul, Korea
| | - Hyun-Seob Lee
- Genomic Core Facility, Transdisciplinary Research and Collaboration Division, Translational Research Institute, and Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Jongho Heo
- National Assembly Futures Institute, Seoul, Korea
| | - Chung Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Nayoung K D Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.,Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Kyu Beck Lee
- Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kook-Hwan Oh
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Yun Kyu Oh
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Korea.
| | - Curie Ahn
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.
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Cornec-Le Gall E, Blais JD, Irazabal MV, Devuyst O, Gansevoort RT, Perrone RD, Chapman AB, Czerwiec FS, Ouyang J, Heyer CM, Senum SR, Le Meur Y, Torres VE, Harris PC. Can we further enrich autosomal dominant polycystic kidney disease clinical trials for rapidly progressive patients? Application of the PROPKD score in the TEMPO trial. Nephrol Dial Transplant 2019; 33:645-652. [PMID: 28992127 PMCID: PMC5888998 DOI: 10.1093/ndt/gfx188] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/13/2017] [Indexed: 01/22/2023] Open
Abstract
Background The PROPKD score has been proposed to stratify the risk of progression to end-stage renal disease in autosomal dominant polycystic kidney disease (ADPKD) subjects. We aimed to assess its prognostic value in a genotyped subgroup of subjects from the Tolvaptan Phase 3 Efficacy and Safety Study in Autosomal Dominant Polycystic Kidney Disease (TEMPO3/4) trial. Methods In the post hoc analysis, PKD1 and PKD2 were screened in 770 subjects and the PROPKD score was calculated in mutation-positive subjects (male: 1 point; hypertension <35 years: 2 points; first urologic event <35 years: 2 points; nontruncating PKD1 mutation: 2 points; truncating PKD1 mutation: 4 points). Subjects were classified into low-risk (LR; 0-3 points), intermediate-risk (IR; 4-6 points) and high-risk (HR; 7-9 points) groups. Results The PROPKD score was calculated in 749 subjects (LR = 132, IR = 344 and HR = 273); age was inversely related to risk (LR = 43.6 years, IR = 39.5 years, HR = 36.2 years; P < 0.001). Subjects from the HR group had significantly higher height-adjusted total kidney volume (TKV) and rates of TKV growth. While baseline renal function was similar across all risk groups, the rate of estimated glomerular filtration rate (eGFR) decline significantly increased from LR to HR in the placebo group. Tolvaptan treatment effectiveness to reduce TKV growth was similar in all three risk categories. While tolvaptan significantly slowed eGFR decline in the IR (tolvaptan = -2.34 versus placebo = -3.33 mL/min/1.73 m2/year; P = 0.008) and HR groups (tolvaptan = -2.74 versus placebo = -3.94 mL/min/1.73 m2/year; P = 0.002), there was no difference in the LR group (tolvaptan = -2.35 versus placebo = -2.50 mL/min/1.73 m2/year; P = 0.72). Excluding the LR subjects from the analysis improved the apparent treatment effect of tolvaptan on eGFR decline. Conclusion This study confirms the prognostic value of the PROPKD score and suggests that it could reduce costs and enhance endpoint sensitivity by enriching future study populations for rapidly progressing ADPKD subjects.
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Affiliation(s)
- Emilie Cornec-Le Gall
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55902, USA.,European University of Western Brittany, CHU Brest, Brest, France
| | | | - Maria V Irazabal
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55902, USA
| | - Olivier Devuyst
- Institute of Nephrology, University of Zurich, Zurich, Switzerland
| | - Ron T Gansevoort
- Department of Nephrology, University Medical Center of Groningen, Groningen, The Netherlands
| | | | | | | | | | - Christina M Heyer
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55902, USA
| | - Sarah R Senum
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55902, USA
| | - Yannick Le Meur
- European University of Western Brittany, CHU Brest, Brest, France
| | - Vicente E Torres
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55902, USA
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55902, USA
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Ranjzad F, Tara A, Basiri A, Aghdami N, Moghadasali R. Co-segregation of candidate polymorphism rs201204878 of the PKD1 gene in a large Iranian family with autosomal dominant polycystic disease. Exp Ther Med 2019; 18:1345-1349. [PMID: 31384335 DOI: 10.3892/etm.2019.7693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 09/01/2018] [Indexed: 11/06/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the fourth most common cause of end-stage renal disease, occurring at a frequency of 1 in 400 to 1 in 800 individuals among different populations. The disease affects all ethnic groups worldwide, and there is a requirement for population-based studies to be conducted in order to improve diagnosis, genetic counseling and treatment. A large Iranian family with ADPKD was recruited for the current study. Clinical evaluation was performed to diagnose and assess disease progression in 11 members of this family, including 7 affected members and 4 unaffected members. PKD1 and PKD2 genes were genotyped in subjects by next-generation sequencing (NGS). Mutational analysis of PKD1 and PKD2 genes in this family revealed three intronic variations and three synonymous exonic variants in the PKD2 gene, and two non-synonymous exonic variants and eight intronic variants in PKD1, resulting in a total of 16 heterozygous variations among these two genes. Among the 16 variations, all except three intronic variants in the PKD1 gene have already reported in the Iranian population. The three novel mutations were predicted to be deleterious polymorphisms using in silico methods. Among the reported intronic variations, rs201204878 was identified as a splice region variant, leading to truncation of the polycystin-1 protein. In conclusion, genotyping of PKD1 and PKD2 in this family with ADPKD revealed no mutational hot spots. However, genetic screening identified three novel variants in the Iranian population. The data generated in the present study will contribute to improving the diagnosis, genetic counseling and treatment of patients with ADPKD.
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Affiliation(s)
- Fariba Ranjzad
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran-1666677951, Islamic Republic of Iran
| | - Ahmad Tara
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran-1666677951, Islamic Republic of Iran
| | - Abbas Basiri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran-1666677951, Islamic Republic of Iran
| | - Nasser Aghdami
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran-8158968433, Islamic Republic of Iran.,Department of Regenerative Biomedicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran-8158968433, Islamic Republic of Iran
| | - Reza Moghadasali
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran-8158968433, Islamic Republic of Iran.,Department of Regenerative Biomedicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran-8158968433, Islamic Republic of Iran
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Identification of a novel COL4A5 mutation in the proband initially diagnosed as IgAN from a Chinese family with X-linked Alport syndrome. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1572-1579. [PMID: 31209800 DOI: 10.1007/s11427-018-9545-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/16/2019] [Indexed: 01/20/2023]
Abstract
Alport syndrome (AS) is a hereditary progressive nephropathy characterized by hematuria, ultrastructural lesions of the glomerular basement membrane, ocular lesions and sensorineural hearing loss. Germline mutations of COL4A5 are associated with X-linked AS with an extreme phenotypic heterogeneity. Here, we investigated a Chinese family with Alport syndrome. The proband was a 9-year-old boy with hematuria and proteinuria. Based on the test results of renal biopsy and immunofluorescence, the proband was initially diagnosed as IgA nephropathy and the treatment was recommended accordingly. Meanwhile, we found that the treatment outcome was poor. Therefore, for proper clinical diagnosis and appropriate treatment, targeted exome-based next-generation sequencing has been undertaken. We identified a novel hemizygous single nucleotide deletion c.1902delA in COL4A5 gene. Segregation analysis identified that this novel mutation is co-segregated among the affected family members but absent in unaffected family members. The clinical diagnosis of the proband was revised as AS accompanied by IgA nephropathy, which has been rarely reported. Our findings demonstrated the significance of the application of Genetic screening, expanded the mutation spectrum of COL4A5 associated AS patients with atypical renal phenotypes and provided a good lesson to be learned from our detour during the diagnosis.
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Ali H, Al-Mulla F, Hussain N, Naim M, Asbeutah AM, AlSahow A, Abu-Farha M, Abubaker J, Al Madhoun A, Ahmad S, Harris PC. PKD1 Duplicated regions limit clinical Utility of Whole Exome Sequencing for Genetic Diagnosis of Autosomal Dominant Polycystic Kidney Disease. Sci Rep 2019; 9:4141. [PMID: 30858458 PMCID: PMC6412018 DOI: 10.1038/s41598-019-40761-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 02/21/2019] [Indexed: 12/18/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is an inherited monogenic renal disease characterised by the accumulation of clusters of fluid-filled cysts in the kidneys and is caused by mutations in PKD1 or PKD2 genes. ADPKD genetic diagnosis is complicated by PKD1 pseudogenes located proximal to the original gene with a high degree of homology. The next generation sequencing (NGS) technology including whole exome sequencing (WES) and whole genome sequencing (WGS), is becoming more affordable and its use in the detection of ADPKD mutations for diagnostic and research purposes more widespread. However, how well does NGS technology compare with the Gold standard (Sanger sequencing) in the detection of ADPKD mutations? Is a question that remains to be answered. We have evaluated the efficacy of WES, WGS and targeted enrichment methodologies in detecting ADPKD mutations in the PKD1 and PKD2 genes in patients who were clinically evaluated by ultrasonography and renal function tests. Our results showed that WES detected PKD1 mutations in ADPKD patients with 50% sensitivity, as the reading depth and sequencing quality were low in the duplicated regions of PKD1 (exons 1–32) compared with those of WGS and target enrichment arrays. Our investigation highlights major limitations of WES in ADPKD genetic diagnosis. Enhancing reading depth, quality and sensitivity of WES in the PKD1 duplicated regions (exons 1–32) is crucial for its potential diagnostic or research applications.
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Affiliation(s)
- Hamad Ali
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Health Sciences Center, Kuwait University, Jabriya, Kuwait. .,Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait. .,Division of Nephrology, Mubarak Al-Kabeer Hospital, Ministry of Health, Jabriya, Kuwait.
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait.
| | - Naser Hussain
- Division of Nephrology, Mubarak Al-Kabeer Hospital, Ministry of Health, Jabriya, Kuwait
| | - Medhat Naim
- Division of Nephrology, Mubarak Al-Kabeer Hospital, Ministry of Health, Jabriya, Kuwait
| | - Akram M Asbeutah
- Department of Radiological Sciences, Faculty of Allied Health Sciences, Health Sciences Center, Kuwait University, Jabriya, Kuwait
| | - Ali AlSahow
- Division of Nephrology, Al-Jahra Hospital, Ministry of Health, Al-Jahra, Kuwait
| | - Mohamed Abu-Farha
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Ashraf Al Madhoun
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Sajjad Ahmad
- Department of Cornea and External Diseases, Moorfields Eye Hospital-NHS Foundation Trust, London, United Kingdom.,Institute of Ophthalmology, University Collage London (UCL), London, United Kingdom
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, USA
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Ranjzad F, Aghdami N, Tara A, Mohseni M, Moghadasali R, Basiri A. Identification of Three Novel Frameshift Mutations in the PKD1 Gene in Iranian Families with Autosomal Dominant Polycystic Kidney Disease Using Efficient Targeted Next-Generation Sequencing. Kidney Blood Press Res 2018; 43:471-478. [PMID: 29590654 DOI: 10.1159/000488471] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/14/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common inherited cystic kidney diseases caused by mutations in two large multi-exon genes, PKD1 and PKD2. High allelic heterogeneity and duplication of PKD1 exons 1-32 as six pseudo genes on chromosome 16 complicate molecular analysis of this disease. METHODS We applied targeted next-generation sequencing (NGS) in 9 non-consanguineous unrelated Iranian families with ADPKD to identify the genes hosting disease-causing mutations. This approach was confirmed by Sanger sequencing. RESULTS Here, we determined three different novel frameshift mutations and four previously reported nonsense mutations in the PKD1 gene encoding polycystin1 in heterozygotes. CONCLUSION This study demonstrates the effectiveness of NGS in significantly reducing the cost and time for simultaneous sequence analysis of PKD1 and PKD2, simplifying the genetic diagnostics of ADPKD. Although a probable correlation between the mutation types and phenotypic outcome is possible, however for more extensive studies in future, the consideration of renal hypouricemia (RHUC) and PKD1 coexistence may be helpful. The novel frameshift mutations reported by this study are p. Q1997X, P. D73X and p. V336X.
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Affiliation(s)
- Fariba Ranjzad
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nasser Aghdami
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Ahmad Tara
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Moghadasali
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Regenerative Biomedicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Tehran, Iran
| | - Abbas Basiri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Xu D, Ma Y, Gu X, Bian R, Lu Y, Xing X, Mei C. Novel Mutations in the PKD1 and PKD2 Genes of Chinese Patients with Autosomal Dominant Polycystic Kidney Disease. Kidney Blood Press Res 2018. [DOI: 10.1159/000487899] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Mimura I, Tanaka T, Nangaku M. New insights into molecular mechanisms of epigenetic regulation in kidney disease. Clin Exp Pharmacol Physiol 2017; 43:1159-1167. [PMID: 27560313 DOI: 10.1111/1440-1681.12663] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 08/12/2016] [Accepted: 08/21/2016] [Indexed: 12/11/2022]
Abstract
The number of patients with kidney failure has increased in recent years. Different factors contribute to the progression of chronic kidney disease, including glomerular sclerosis, atherosclerosis of the renal arteries and tubulointerstitial fibrosis. Tubulointerstitial injury is induced by hypoxia and other inflammatory signals, leading to fibroblast activation. Technological advances using high-throughput sequencing has enabled the determination of the expression profile of almost all genes, revealing that gene expression is intricately regulated by DNA methylation, histone modification, changes in chromosome conformation, long non-coding RNAs and microRNAs. These epigenetic modifications are stored as cellular epigenetic memory. Epigenetic memory leads to adult-onset disease or ageing in the long term and may possibly play an important role in the kidney disease process. Herein we emphasize the importance of clarifying the molecular mechanisms underlying epigenetic modifications because this may lead to the development of new therapeutic targets in kidney disease.
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Affiliation(s)
- Imari Mimura
- Division of Nephrology and Endocrinology, The University of Tokyo, Tokyo, Japan
| | - Tetsuhiro Tanaka
- Division of Nephrology and Endocrinology, The University of Tokyo, Tokyo, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, The University of Tokyo, Tokyo, Japan
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Cornec-Le Gall E, Audrézet MP, Renaudineau E, Hourmant M, Charasse C, Michez E, Frouget T, Vigneau C, Dantal J, Siohan P, Longuet H, Gatault P, Ecotière L, Bridoux F, Mandart L, Hanrotel-Saliou C, Stanescu C, Depraetre P, Gie S, Massad M, Kersalé A, Séret G, Augusto JF, Saliou P, Maestri S, Chen JM, Harris PC, Férec C, Le Meur Y. PKD2-Related Autosomal Dominant Polycystic Kidney Disease: Prevalence, Clinical Presentation, Mutation Spectrum, and Prognosis. Am J Kidney Dis 2017; 70:476-485. [PMID: 28356211 DOI: 10.1053/j.ajkd.2017.01.046] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 01/12/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND PKD2-related autosomal dominant polycystic kidney disease (ADPKD) is widely acknowledged to be of milder severity than PKD1-related disease, but population-based studies depicting the exact burden of the disease are lacking. We aimed to revisit PKD2 prevalence, clinical presentation, mutation spectrum, and prognosis through the Genkyst cohort. STUDY DESIGN Case series, January 2010 to March 2016. SETTINGS & PARTICIPANTS Genkyst study participants are individuals older than 18 years from 22 nephrology centers from western France with a diagnosis of ADPKD based on Pei criteria or at least 10 bilateral kidney cysts in the absence of a familial history. Publicly available whole-exome sequencing data from the ExAC database were used to provide an estimate of the genetic prevalence of the disease. OUTCOMES Molecular analysis of PKD1 and PKD2 genes. Renal survival, age- and sex-adjusted estimated glomerular filtration rate. RESULTS The Genkyst cohort included 293 patients with PKD2 mutations (203 pedigrees). PKD2 patients with a nephrology follow-up corresponded to 0.63 (95% CI, 0.54-0.72)/10,000 in Brittany, while PKD2 genetic prevalence was calculated at 1.64 (95% CI, 1.10-3.51)/10,000 inhabitants in the European population. Median age at diagnosis was 42 years. Flank pain was reported in 38.9%; macroscopic hematuria, in 31.1%; and cyst infections, in 15.3% of patients. At age 60 years, the cumulative probability of end-stage renal disease (ESRD) was 9.8% (95% CI, 5.2%-14.4%), whereas the probability of hypertension was 75.2% (95% CI, 68.5%-81.9%). Although there was no sex influence on renal survival, men had lower kidney function than women. Nontruncating mutations (n=36) were associated with higher age-adjusted estimated glomerular filtration rates. Among the 18 patients with more severe outcomes (ESRD before age 60), 44% had associated conditions or nephropathies likely to account for the early progression to ESRD. LIMITATIONS Younger patients and patients presenting with milder forms of PKD2-related disease may not be diagnosed or referred to nephrology centers. CONCLUSIONS Patients with PKD2-related ADPKD typically present with mild disease. In case of accelerated degradation of kidney function, a concomitant nephropathy should be ruled out.
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Affiliation(s)
- Emilie Cornec-Le Gall
- Service de Néphrologie, Centre Hospitalier Régional Universitaire de Brest, Brest, France; Université européenne de Bretagne, Université de Bretagne Occidentale, Brest, France; Institut National de la Santé et de la Recherche Médicale, Unité 1078, Brest, France; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN.
| | - Marie-Pierre Audrézet
- Institut National de la Santé et de la Recherche Médicale, Unité 1078, Brest, France; Laboratoire de Génétique et Génomique Fonctionnelle et Biotechnologies, Centre Hospitalier Régional Universitaire de Brest, Brest, France
| | - Eric Renaudineau
- Service de Néphrologie, Centre Hospitalier Broussais, Saint Malo, France
| | - Maryvonne Hourmant
- Service de Néphrologie-Immunologie Clinique, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Christophe Charasse
- Service de Néphrologie, Centre Hospitalier Yves Le Foll, Saint Brieuc, France
| | - Eric Michez
- Service de Néphrologie, Centre Hospitalier de Bretagne Atlantique, Vannes, France
| | - Thierry Frouget
- Service de Néphrologie, Centre Hospitalier Universitaire Pontchaillou, Rennes, France
| | - Cécile Vigneau
- Service de Néphrologie, Centre Hospitalier Universitaire Pontchaillou, Rennes, France
| | - Jacques Dantal
- Service de Néphrologie-Immunologie Clinique, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Pascale Siohan
- Service de Néphrologie, Centre Hospitalier de Cornouaille, Quimper, France
| | - Hélène Longuet
- Service de Néphrologie, Centre Hospitalier Universitaire de Tours, Tours, France
| | - Philippe Gatault
- Service de Néphrologie, Centre Hospitalier Universitaire de Tours, Tours, France
| | - Laure Ecotière
- Service de Néphrologie, Centre Hospitalier Universitaire de Poitiers, Poitiers, France
| | - Frank Bridoux
- Service de Néphrologie, Centre Hospitalier Universitaire de Poitiers, Poitiers, France
| | - Lise Mandart
- Service de Néphrologie, Centre Hospitalier de Bretagne Atlantique, Vannes, France
| | | | - Corina Stanescu
- Service de Néphrologie, Centre Hospitalier Yves Le Foll, Saint Brieuc, France
| | | | | | - Michiel Massad
- Service de Néphrologie, Centre Hospitalier de Centre Bretagne, Pontivy, France
| | - Aude Kersalé
- Service de Néphrologie, Centre Hospitalier Régional Universitaire de Brest, Brest, France
| | - Guillaume Séret
- Echo, expansion des centres d'hémodialyse de l'Ouest, Le Mans, France
| | | | - Philippe Saliou
- Institut National de la Santé et de la Recherche Médicale, Unité 1078, Brest, France; Laboratoire d'Hygiène et de Santé Publique, Centre Hospitalier Régional Universitaire de Brest, Brest, France
| | - Sandrine Maestri
- Laboratoire de Génétique et Génomique Fonctionnelle et Biotechnologies, Centre Hospitalier Régional Universitaire de Brest, Brest, France
| | - Jian-Min Chen
- Université européenne de Bretagne, Université de Bretagne Occidentale, Brest, France; Institut National de la Santé et de la Recherche Médicale, Unité 1078, Brest, France; Etablissement Français du Sang (EFS) Bretagne, Brest, France
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN
| | - Claude Férec
- Université européenne de Bretagne, Université de Bretagne Occidentale, Brest, France; Institut National de la Santé et de la Recherche Médicale, Unité 1078, Brest, France; Laboratoire de Génétique et Génomique Fonctionnelle et Biotechnologies, Centre Hospitalier Régional Universitaire de Brest, Brest, France; Etablissement Français du Sang (EFS) Bretagne, Brest, France
| | - Yannick Le Meur
- Service de Néphrologie, Centre Hospitalier Régional Universitaire de Brest, Brest, France; Université européenne de Bretagne, Université de Bretagne Occidentale, Brest, France
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11
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Kinoshita M, Higashihara E, Kawano H, Higashiyama R, Koga D, Fukui T, Gondo N, Oka T, Kawahara K, Rigo K, Hague T, Katsuragi K, Sudo K, Takeshi M, Horie S, Nutahara K. Technical Evaluation: Identification of Pathogenic Mutations in PKD1 and PKD2 in Patients with Autosomal Dominant Polycystic Kidney Disease by Next-Generation Sequencing and Use of a Comprehensive New Classification System. PLoS One 2016; 11:e0166288. [PMID: 27835667 PMCID: PMC5105999 DOI: 10.1371/journal.pone.0166288] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 10/26/2016] [Indexed: 01/06/2023] Open
Abstract
Genetic testing of PKD1 and PKD2 is expected to play an increasingly important role in determining allelic influences in autosomal dominant polycystic kidney disease (ADPKD) in the near future. However, to date, genetic testing is not commonly employed because it is expensive, complicated because of genetic heterogeneity, and does not easily identify pathogenic variants. In this study, we developed a genetic testing system based on next-generation sequencing (NGS), long-range polymerase chain reaction, and a new software package. The new software package integrated seven databases and provided access to five cloud-based computing systems. The database integrated 241 polymorphic nonpathogenic variants detected in 140 healthy Japanese volunteers aged >35 years, who were confirmed by ultrasonography as having no cysts in either kidney. Using this system, we identified 60 novel and 30 known pathogenic mutations in 101 Japanese patients with ADPKD, with an overall detection rate of 89.1% (90/101) [95% confidence interval (CI), 83.0%-95.2%]. The sensitivity of the system increased to 93.1% (94/101) (95% CI, 88.1%-98.0%) when combined with multiplex ligation-dependent probe amplification analysis, making it sufficient for use in a clinical setting. In 82 (87.2%) of the patients, pathogenic mutations were detected in PKD1 (95% CI, 79.0%-92.5%), whereas in 12 (12.8%) patients pathogenic mutations were detected in PKD2 (95% CI, 7.5%-21.0%); this is consistent with previously reported findings. In addition, we were able to reconfirm our pathogenic mutation identification results using Sanger sequencing. In conclusion, we developed a high-sensitivity NGS-based system and successfully employed it to identify pathogenic mutations in PKD1 and PKD2 in Japanese patients with ADPKD.
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Affiliation(s)
| | - Eiji Higashihara
- Department of ADPKD Research, School of Medicine, Kyorin University, Tokyo, Japan
- Department of Urology, School of Medicine, Kyorin University, Tokyo, Japan
| | - Haruna Kawano
- Department of Urology, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Ryo Higashiyama
- Diagnostic Division, Otsuka Pharmaceutical Co., Ltd., Tokushima, Japan
| | - Daisuke Koga
- Diagnostic Division, Otsuka Pharmaceutical Co., Ltd., Tokushima, Japan
| | | | | | | | | | | | | | | | - Kimiyoshi Sudo
- Diagnostic Division, Otsuka Pharmaceutical Co., Ltd., Tokushima, Japan
| | | | - Shigeo Horie
- Department of Urology, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kikuo Nutahara
- Department of Urology, School of Medicine, Kyorin University, Tokyo, Japan
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12
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System analysis of gene mutations and clinical phenotype in Chinese patients with autosomal-dominant polycystic kidney disease. Sci Rep 2016; 6:35945. [PMID: 27782177 PMCID: PMC5080601 DOI: 10.1038/srep35945] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/07/2016] [Indexed: 02/05/2023] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disorder mainly caused by mutation in PKD1/PKD2. However, ethnic differences in mutations, the association between mutation genotype/clinical phenotype, and the clinical applicable value of mutation detection are poorly understood. We made systematically analysis of Chinese ADPKD patients based on a next-generation sequencing platform. Among 148 ADPKD patients enrolled, 108 mutations were detected in 127 patients (85.8%). Compared with mutations in Caucasian published previously, the PKD2 mutation detection rate was lower, and patients carrying the PKD2 mutation invariably carried the PKD1 mutation. The definite pathogenic mutation detection rate was lower, whereas the multiple mutations detection rate was higher in Chinese patients. Then, we correlated PKD1/PKD2 mutation data and clinical data: patients with mutation exhibited a more severe phenotype; patients with >1 mutations exhibited a more severe phenotype; patients with pathogenic mutations exhibited a more severe phenotype. Thus, the PKD1/PKD2 mutation status differed by ethnicity, and the PKD1/PKD2 genotype may affect the clinical phenotype of ADPKD. Furthermore, it makes sense to detect PKD1/PKD2 mutation status for early diagnosis and prognosis, perhaps as early as the embryo/zygote stage, to facilitate early clinical intervention and family planning.
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13
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Xue C, Zhou CC, Wu M, Mei CL. The Clinical Manifestation and Management of Autosomal Dominant Polycystic Kidney Disease in China. KIDNEY DISEASES 2016; 2:111-119. [PMID: 27921038 DOI: 10.1159/000449030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 08/10/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is the most common monogenic hereditary kidney disease characterized by progressive enlargement of renal cysts. The incidence is 1-2‰ worldwide. Mutations in two genes (PKD1 and PKD2) cause ADPKD. Currently, there is no pharmaceutical treatment available for ADPKD patients in China. Summary: This review focused on advances in clinical manifestation, gene diagnosis, risk factors, and management of ADPKD in China. There is an age-dependent increase in total kidney volume (TKV) and decrease in renal function in Chinese ADPKD patients. ADPKD is more severe in males than in females. Great progress has been made in molecular diagnosis in the last two decades. Nephrologists found many novel PKD mutations in Chinese ADPKD patients early through polymerase chain reaction, and then through liquid chromatography in 2000s, and recently through next-generation sequencing. Major predictive factors for ADPKD progression are age, PKD genotype, sex, estimated glomerular filtration rate (eGFR), and TKV. With respect to the management of ADPKD, inhibitors targeting mTOR and cAMP are the focus of clinical trials. Triptolide has been used to treat ADPKD patients in clinical trials in China. Triptolide significantly protected eGFR of ADPKD patients compared with placebo. KEY MESSAGES ADPKD affects about 1.5 million people in China. An additional PKD gene besides PKD1 and PKD2 was not found in the Chinese. The prevalence of intracranial aneurysm in Chinese ADPKD patients was 12.4%. The predictive factors for eGFR decrease in Chinese ADPKD patients are TKV, proteinuria, history of hypertension, and age. The treatment strategies in clinical trials for ADPKD patients in China are similar to those in the West except for triptolide. FACTS FROM EAST AND WEST (1) ADPKD is diagnosed globally by ultrasound detection of kidney enlargement and presence of cysts. Recent analyses of variants of the PKD1 and PKD2 genes by next-generation sequencing in Chinese and Western ADPKD patients might lead to the development of reliable genetic tests. (2) Besides lifestyle changes (low-salt diet, sufficient fluid intake, and no smoking), blood pressure control is the primary nonspecific treatment recommended by Kidney Disease - Improving Global Outcomes (KDIGO) for ADPKD patients. How low the blood pressure target should be and what the means of achieving it are remain open questions depending on the severity of chronic kidney disease and the age of the patients. In a recent Chinese study, diagnostic needle aspiration and laparoscopic unroofing surgery successfully improved infection, pain, and hypertension. Peritoneal dialysis was found to be a feasible treatment for most Chinese ADPKD patients with end-stage renal disease. In most Western centers, patients without contraindication are selected for peritoneal dialysis. Kidney transplantation with concurrent bilateral nephrectomy was successful in relieving hypertension and infection in Chinese ADPKD patients. In Western countries, sequential surgical intervention with kidney transplantation after nephrectomy, or the other way round, is preferred in order to reduce risks. (3) The vasopressin 2 receptor antagonist tolvaptan was approved in Europe, Canada, Japan, and Korea to slow down progression of kidney disease in ADPKD patients. Tolvaptan is not yet approved in the USA or in China. mTOR pathway-targeting drugs are currently under evaluation: mTOR inhibitors could slow down the increase in total kidney volume in a cohort of Western and Japanese ADPKD patients. Western studies as well as an ongoing study in China failed to show benefit from rapamycin. A study performed in Italy indicates protective effects of the somatostatin analog octreotide in ADPKD patients. Western and Chinese studies revealed a potential beneficial effect of triptolide, the active substance of the traditional Chinese medicine Tripterygium wilfordii (Lei Gong Teng) to prevent worsening in ADPKD patients.
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Affiliation(s)
- Cheng Xue
- Division of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Chen-Chen Zhou
- Division of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Ming Wu
- Division of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Chang-Lin Mei
- Division of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, China
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14
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Liu B, Chen SC, Yang YM, Yan K, Qian YQ, Zhang JY, Hu YT, Dong MY, Jin F, Huang HF, Xu CM. Identification of novel PKD1 and PKD2 mutations in a Chinese population with autosomal dominant polycystic kidney disease. Sci Rep 2015; 5:17468. [PMID: 26632257 PMCID: PMC4668380 DOI: 10.1038/srep17468] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/30/2015] [Indexed: 02/08/2023] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is one of the most frequently inherited renal diseases caused by mutations in PKD1 and PKD2. We performed mutational analyses of PKD genes in 49 unrelated patients using direct PCR-sequencing and multiplex ligation-dependent probe amplification (MLPA) for PKD1 and PKD2. RT-PCR analysis was also performed in a family with a novel PKD2 splicing mutation. Disease-causing mutations were identified in 44 (89.8%) of the patients: 42 (95.5%) of the patients showed mutations in PKD1, and 2 (4.5%) showed mutations in PKD2. Ten nonsense, 17 frameshift, 4 splicing and one in-frame mutation were found in 32 of the patients. Large rearrangements were found in 3 patients, and missense mutations were found in 9 patients. Approximately 61.4% (27/44) of the mutations are first reported with a known mutation rate of 38.6%. RNA analysis of a novel PKD2 mutation (c.595_595 + 14delGGTAAGAGCGCGCGA) suggested monoallelic expression of the wild-type allele. Furthermore, patients with PKD1-truncating mutations reached end-stage renal disease (ESRD) earlier than patients with non-truncating mutations (47 ± 3.522 years vs. 59 ± 11.687 years, P = 0.016). The mutation screening of PKD genes in Chinese ADPKD patients will enrich our mutation database and significantly contribute to improve genetic counselling for ADPKD patients.
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Affiliation(s)
- Bei Liu
- Women's Hospital School of Medicine Zhejiang University, Hangzhou 310006, P. R. China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, P. R. China
| | - Song-Chang Chen
- Institute of Embryo-Fetal Original Adult Disease Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P.R. China.,The International Peace Maternity &Child Health Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P. R. China
| | - Yan-Mei Yang
- Women's Hospital School of Medicine Zhejiang University, Hangzhou 310006, P. R. China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, P. R. China
| | - Kai Yan
- Women's Hospital School of Medicine Zhejiang University, Hangzhou 310006, P. R. China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, P. R. China
| | - Ye-Qing Qian
- Women's Hospital School of Medicine Zhejiang University, Hangzhou 310006, P. R. China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, P. R. China
| | - Jun-Yu Zhang
- Institute of Embryo-Fetal Original Adult Disease Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P.R. China.,The International Peace Maternity &Child Health Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P. R. China
| | - Yu-Ting Hu
- Institute of Embryo-Fetal Original Adult Disease Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P.R. China.,The International Peace Maternity &Child Health Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P. R. China
| | - Min-Yue Dong
- Women's Hospital School of Medicine Zhejiang University, Hangzhou 310006, P. R. China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, P. R. China
| | - Fan Jin
- Women's Hospital School of Medicine Zhejiang University, Hangzhou 310006, P. R. China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, P. R. China
| | - He-Feng Huang
- Women's Hospital School of Medicine Zhejiang University, Hangzhou 310006, P. R. China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, P. R. China.,Institute of Embryo-Fetal Original Adult Disease Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P.R. China.,The International Peace Maternity &Child Health Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P. R. China
| | - Chen-Ming Xu
- Women's Hospital School of Medicine Zhejiang University, Hangzhou 310006, P. R. China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou 310006, P. R. China.,Institute of Embryo-Fetal Original Adult Disease Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P.R. China.,The International Peace Maternity &Child Health Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P. R. China
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15
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Yu G, Qian X, Wu Y, Li X, Chen J, Xu J, Qi J. Analysis of gene mutations in PKD1/PKD2 by multiplex ligation-dependent probe amplification: some new findings. Ren Fail 2015; 37:366-71. [PMID: 26381842 DOI: 10.3109/0886022x.2015.1088349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is a serious genetic disorder that can lead to chronic renal disease. Protein dysfunction caused by mutations in the genes polycystic kidney disease 1 (PKD1) and polycystic kidney disease 2 (PKD2) is an important factor in the pathogenesis of ADPKD. In the present study, 30 Chinese patients with confirmed diagnosis of ADPKD, based on ultrasound or computerized tomography (CT) findings were selected, and the exon copy numbers of PKD1 and PKD2 were determined using multiplex ligation-dependent probe amplification (MLPA). MLPA identified exon deletion in 1 case, suspected exon deletion in 4 cases, and suspected duplications in 3 cases. One case of suspected exon deletion was confirmed using quantitative real-time polymerase chain reaction (q-PCR) and sequencing (PKD2 exon 8). A missense mutation was observed in 1 case of exon deletion using q-PCR and sequencing (PKD1 exon 40, c.11333 C>A). The cases of suspected duplications were verified by q-PCR, and the copy number of exon 6 of PKD1 in 1 case of suspected duplication was 3.8 times greater than that in normal controls. Our findings provide new insights into ADPKD screening and mark a possibly meaningful step toward improved diagnosis and treatment of patients with ADPKD.
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Affiliation(s)
- Guopeng Yu
- a Department of Urology , Xinhua Hospital, School of Medicine, Shanghai Jiaotong University , Shanghai , P.R. China .,b Fudan Institute of Urology, Fudan University , Shanghai , P.R. China .,c Department of Urology , Huashan Hospital, Fudan University , Shanghai , P.R. China , and
| | - Xiaoqiang Qian
- a Department of Urology , Xinhua Hospital, School of Medicine, Shanghai Jiaotong University , Shanghai , P.R. China
| | - Yu Wu
- a Department of Urology , Xinhua Hospital, School of Medicine, Shanghai Jiaotong University , Shanghai , P.R. China
| | - Xinjuan Li
- d Medical examination center, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University , Shanghai , P.R. China
| | - Jianhua Chen
- a Department of Urology , Xinhua Hospital, School of Medicine, Shanghai Jiaotong University , Shanghai , P.R. China
| | - Jianfeng Xu
- b Fudan Institute of Urology, Fudan University , Shanghai , P.R. China .,c Department of Urology , Huashan Hospital, Fudan University , Shanghai , P.R. China , and
| | - Jun Qi
- a Department of Urology , Xinhua Hospital, School of Medicine, Shanghai Jiaotong University , Shanghai , P.R. China
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16
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Iorio A, Polimanti R, Calandro M, Graziano ME, Piacentini S, Bucossi S, Squitti R, Lazzarin N, Scano G, Limbruno GM, Manfellotto D, Fuciarelli M. Explorative genetic association study of GSTT2B copy number variant in complex disease risks. Ann Hum Biol 2015. [PMID: 26207597 DOI: 10.3109/03014460.2015.1049206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Glutathione S-transferases (GSTs) are the main phase II enzymes involved in cellular detoxification. Through phase I and phase II detoxification reactions, the cell is able to detoxify endogenous and exogenous toxic compounds. AIMS This study focused attention on the GSTT2B copy number variant (CNV) in order to explore its involvement in the genetic pre-disposition to asthma, Alzheimer's disease (AD), allergic rhinitis (AR), essential hypertension (EH), hypothyroidism and recurrent miscarriage (RM). METHODS The study population consists of 1225 individuals divided into six case-control groups. The genotyping of the GSTT2B CNV was performed by using a duplex-PCR. Odds Ratios (ORs) were calculated, adjusting for the confounding variables, to estimate the association between GSTT2B CNV and the disease status. RESULTS The χ(2)-test and ORs did not show any association between this genetic marker and pathological phenotypes. CONCLUSION The data highlights that GSTT2B CNV is not associated with the investigated complex diseases in Italian patients. However, further investigations are necessary to replicate these findings in larger sample sizes and to explore other health-related phenotypes.
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Affiliation(s)
- Andrea Iorio
- a Department of Biology , University of Rome 'Tor Vergata' , Rome , Italy
| | - Renato Polimanti
- b Department of Psychiatry , Yale University School of Medicine , West Haven , CT , USA
| | - Melania Calandro
- a Department of Biology , University of Rome 'Tor Vergata' , Rome , Italy
| | | | - Sara Piacentini
- a Department of Biology , University of Rome 'Tor Vergata' , Rome , Italy
| | - Serena Bucossi
- c Department of Clinical Neuroscience , AFaR - 'San Giovanni Calibita' Fatebenefratelli Hospital , Isola Tiberina , Rome , Italy .,d Department of Neurology , 'Campus Bio-Medico' University , Rome , Italy
| | - Rosanna Squitti
- c Department of Clinical Neuroscience , AFaR - 'San Giovanni Calibita' Fatebenefratelli Hospital , Isola Tiberina , Rome , Italy .,e Laboratorio Neurodegenerazione , IRCCS San Raffaele Pisana , Rome , Italy
| | | | - Giuseppina Scano
- a Department of Biology , University of Rome 'Tor Vergata' , Rome , Italy
| | - Giancarlo Maria Limbruno
- g Clinical Pathology Department , AFaR - 'San Giovanni Calibita' Fatebenefratelli Hospital , Rome , Italy
| | | | - Maria Fuciarelli
- a Department of Biology , University of Rome 'Tor Vergata' , Rome , Italy
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17
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Liu W, Chen M, Wei J, He W, Li Z, Sun X, Shi Y. Modification of PCR conditions and design of exon-specific primers for the efficient molecular diagnosis of PKD1 mutations. Kidney Blood Press Res 2014; 39:536-45. [PMID: 25531466 DOI: 10.1159/000368464] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Autosomal-dominant polycystic kidney disease (ADPKD) is a heterogeneous genetic disorder caused by mutations in the PKD1 and PKD2 genes. Currently, long-range PCR followed by nested PCR and sequencing (LRNS) is the gold standard approach for PKD1 testing. However, LRNS is complicated by the high structural and sequence complexity of PKD1, which makes the procedure for amplification and analysis of PKD1 difficult. METHODS Here in, we modified the PCR conditions and designed primers for efficient and specific amplification of both the long-range and individual exons of PKD1. RESULTS Using the modified system, seven long-range fragments were specifically amplified using two distinct sets of conditions, and all individual exon PCR assays were easily performed using a touch-down PCR method. Seven pathogenic or likely pathogenic variants, including two novel truncated frameshift indels and two novel likely pathogenic missense mutations, were identified in eight unrelated patients with or without histories of ADPKD disease (one variant was observed in two unrelated patients). Using combined bioinformatics tools, two indeterminate missense variants were identified in two sporadic patients. CONCLUSION Four novel PKD1 variants were identified in this study. We demonstrated that the modified LRNS method achieves high sensitivity and specificity for detecting pathogenic variants of ADPKD.
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Affiliation(s)
- WeiQiang Liu
- Graduate school, Southern Medical University, Guangzhou 510515, China
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